Evolutionary Biology and Ontologies

Introduction

This workshop will held in conjunction with the Evolution 2008 meeting in Minnesota, MN, 20 June 2008. It is organized under the auspices of the National Center for Biomedical Ontologies (NCBO) in collaboration with the National Evolutionary Synthesis Center (NESCent).

Organizers

Barry Smith (Buffalo), Paula Mabee (South Dakota), Todd Vision (North Carolina), Monte Westerfield (Oregon)

Focus

This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

Goals

• (1) Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
• (2) Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
• (3) Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?

Registration Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

Draft Agenda

• 9:00-10.00 Barry Smith, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; Lead Scientist of the National Center for Biomedical Ontology: Tutorial: An Introduction to Ontology for Evolutionary Biology
• 10.00-10.30 Break
• 10.30-11.00 Chris Mungall, University of California, Berkeley: An Introduction to the PATO Phenotype Ontology
• 11:00-11:30 Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases
• 11:30-12:00 Paula Mabee, University of South Dakota: An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics
• 12:00 – 1:00 lunch
• 1.00-1:45 Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, Oregon: An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies
• 1:45-2:15 Anne Maglia, University of Missouri-Rolla: Developing an Ontology for Amphibians using NLP
• 2:15 – 2:45 Coffee
• 2:45 – 3:15 Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina: Ontologies, Image Databases, and Evolutionary Biology
• 3.15—3:45 Todd Vision, Assistant Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina: An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits
• 3:45 – 4:45 Roundtable & Discussion
• 4.45-5:00 Suzanna Lewis and Paula Mabee: Wrap-Up Session: Next Steps

Background Reading

The OBO Foundry

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology for amphibians. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) Ontologies for behavior. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J, Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC (2007) Text linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology 56, 283-94.